Trans Rotamers Research Articles

Resonance enhanced multiphoton ionization spectroscopy and theoretical calculations of cis- and trans-m-aminostyrene rotamers

The ab initio and DFT calculations predict that two rotamers, cis and trans m-aminostyrene, are stable for each of the S0, S1 and D0 states. In the one-color resonant two-photon ionization (1C-R2PI) spectra, the band origins of the S1←S0 electronic transitions (00 band) of cis and trans m-aminostyrene appear respectively at 30,937±3 and 31,141±3cm−1. The electronic transition energies (E1’s) of both rotamers of m-aminostyrene are lower than that of p-aminostyrene, which is contrary to the prediction according to the previous studies. The redshift of E1’s may be related to the mixing character of “1Lb” and “1La” in the S1 states of the two rotamers. The 2C-R2PI spectra give the adiabatic ionization energies of 61,278±15 and 61,495±15cm−1 for cis and trans rotamers. The observed active modes of rotamers in the S1 states involve mainly the in-plane ring deformation and substituent-sensitive bending vibration. It is derived from the 1C- and 2C-R2PI spectroscopic data that the cis rotamer of m-aminostyrene is more stable than the trans rotamer by 30±30, 234±30 and 247±30cm−1 for the S0, S1 and D0 states, respectively. This is different from the m-aminophenol and m-aminoanisole that have a more stable trans rotamer.

REMPI and MATI spectroscopic study of selected cis and trans 3-chlorostyrene rotamers

The ab initio and DFT calculations predict two stable rotamers, cis and trans, for 3-chlorostyrene in each of the S0, S1 and D0 states. In the two-color resonant two-photon ionization (2C-R2PI) spectra, the band origins of S1←S0 electronic transition of cis and trans 3-chlorostyrene appears respectively at 33766±3 and 34061±3cm−1. The mass-analyzed threshold ionization (MATI) spectra give the adiabatic ionization energies of 69701±4cm−1 and 69571±4cm−1 for cis and trans rotamers. Within the experimental detection limit, the measured transition energies are the same for both the 35Cl and 37Cl isotopomers. The observed active modes of rotamers in the S1 and D0 states involve mainly the in-plane ring deformation and substituent-sensitive bending vibration. It is derived from the 2C-R2PI and MATI spectroscopic data that the cis rotamer is more stable than the trans rotamer by 218±30, 513±30 and 88±30cm−1 for the S0, S1 and D0 states, respectively.

Rotamers of 3,4-difluorophenol studied by two-color resonant two-photon mass-analyzed threshold ionization spectroscopy

Abstract We applied the resonant two-photon ionization and mass-analyzed threshold ionization techniques to record the vibrational spectra of 3,4-difluorophenol in the first electronically excited and the ionic ground states. The band origins of the S1 ← S0 electronic transition of the cis and trans rotamers are found to be 35,486 ± 2 and 35,704 ± 2 cm−1 and the adiabatic ionization energies are 70,016 ± 5 and 70,203 ± 5 cm−1, respectively. The distinct spectral features mainly result from the in-plane ring deformation and substituent-sensitive bending vibrations. Spectral analysis suggests that the molecular geometry and vibrational coordinates of the cation in the D0 state resemble those of the neutral species in the S1 state for both cis and trans rotamers.

Rotamers and isotopomers of 3-chloro-5-fluoroanisole studied by resonant two-photon ionization spectroscopy and theoretical calculations

The ab initio and density functional theory (DFT) calculations reveal that two rotamers, denoted by cis and trans 3-chloro-5-fluoroanisole (3C5FA), are stable for each of the S0, S1, and D0 states. In the one-color resonant two-photon ionization (R2PI) spectra, the band origins of the S1←S0 electronic transition (00 bands) of cis35Cl-3C5FA and cis37Cl-3C5FA are both located at 36,468±3cm−1, while the 00 bands of trans35Cl-3C5FA and trans37Cl-3C5FA are found to be 36,351±3 and 36,354±3cm−1. The two rotamers display very similar vibrational frequencies in the S1 state, and the observed active modes mainly involve the in-plane ring deformation vibrations. By the two-color R2PI spectroscopy, the adiabatic ionization energies (IEs) of both isotopomers of 3C5FA are determined to be 69,720±15cm−1 for the cis rotamer and 69,636±15cm−1 for the trans rotamer. The substitution, conformation, and isotope effects on the properties of 3C5FA, including the molecular structures, vibrational frequencies, and electronic transition and ionization energies, were also discussed in detail.

Rotamers of 3,4-difluoroanisole studied by two-color resonant two-photon mass-analyzed threshold ionization spectroscopy

We reported the vibronic and cation spectra of 3,4-difluoroanisole. The band origins of the S1←S0 electronic transition of the cis and trans rotamers appear at 35,505±2 and 35,711±2cm−1 and the adiabatic ionization energies are determined to be 67,780±5 and 68,125±5cm−1, respectively. Most of the observed active vibrations in the electronically excited S1 and cationic ground D0 states mainly involve in-plane ring deformation and substituent-sensitive bending vibrations. Analysis of the obtained vibronic and cation spectra suggests that the molecular geometry, symmetry, and vibrational coordinates of the cation in the D0 state are like those of the neutral species in the S1 state for these two isomeric species.

The Click Triazolium Peptoid Side Chain: A Strong cis-Amide Inducer Enabling Chemical Diversity

Access to homogeneous and discrete folded peptoid structures primarily depends on control of the cis/trans isomerism of backbone tertiary amides. This can be achieved by designing specific side chains capable of forming local interactions with the backbone. This is often undertaken at the expense of side-chain diversity, which is a key advantage of peptoids over other families of peptidomimetics. We report for the first time a positively charged triazolium-type side chain that does not compromise diversity and exhibits the best ability reported to date for inducing the cis conformation. The cis-directing effect was studied in N-acetamide dipeptoid model systems and evaluated in terms of K(cis/trans) using NMR spectroscopy in aprotic and protic solvents. Computational geometry optimization and natural bond orbital analysis in combination with NOESY experiments were consistent with a model in which n → π*(Ar) electronic delocalization [from carbonyl (O(i-1)) to the antibonding orbital (π*) of the triazolium motif on residue i] may be operative. In the computational model (gas-phase) and experimentally in CDCl(3), H-bonding between the triazolium C-H proton and the C(i)═O(i) oxygen was also identified and may act cooperatively with the n → π*(Ar) delocalization, resulting in the absence of the trans rotamers in CDCl(3).

Rotamers of m-fluoroanisole studied by two-color resonant two-photon mass-analyzed threshold ionization spectroscopy

We report the cation spectra of the cis and trans rotamers of m-fluoroanisole, recorded by using the two-color resonant two-photon mass-analyzed threshold ionization spectroscopic technique. The adiabatic ionization energies of the cis and trans rotamers are 67867±5 and 68304±5cm−1, respectively. The observed active vibrations 6b, 6a, 1, and 12 are found to have frequencies of 473, 549, 714, and 955cm−1 for the cis rotamer and 463, 565, 714, and 962cm−1 for the trans rotamer of m-fluoroanisole in the cationic ground state, respectively. These results show that the frequency depends on the nature, vibrational pattern, relative orientation and the extent of the F and OCH3 substituents participation in the normal vibration.

2-Chloro- and 2-bromo-3-pyridinecarboxaldehydes: Structures, rotamers, fermi resonance and vibration modes

FT-Infrared (4000–400 cm −1) and NIR-FT-Raman (4000–50 cm −1) spectral measurements have been made for 2-chloro- and 2-bromo-3-pyridinecarboxaldehydes. A DFT vibration analysis at B3LYP/6-311++G (d,p) level, valence force-fields and vibrational mode calculations have been performed. Aided by very good agreement between observed and computed vibration spectra, a complete assignment of fundamental vibration modes to the observed absorptions and Raman bands has been proposed. Orientations of the aldehydic group have produced two oblate asymmetric rotamers for each molecule, ON- trans and ON- cis: the ON- trans rotamer being more stable than cis by 3.42 kcal mol −1 for 2-chloro-3-pyridinecarboxaldehyde and 3.68 kcal mol −1 for 2-bromo-3-pyridinecarboxaldehyde. High potential energy barrier ca 14 kcal/mol, induced by steric hindrance, restricts rotamers’ population to ON- trans only. It is observed that, in the presence of bromine, C–H stretching modes are pronounced; a missing characteristic ring mode in chlorine's presence shows at 1557 cm −1; the characteristic ring mode at 1051 cm −1 is diminished; a mixed mode near 707 cm −1 is enhanced. Further, an observed doublet near 1696–1666 cm −1 in both IR and Raman spectra is explained on the basis of Fermi resonance between aldehydic carbonyl stretching at 1696 cm −1 and a combination mode of ring stretch near 1059 cm −1 and deformation vibration, 625 cm −1. A strong Raman aldehydic torsional mode at 62 cm −1 is interpreted to correspond to the dominant ON- trans over cis rotamers population.

Theoretical Study of the Gauche and Trans Conformers of SiH2X–CH2X, SiH2F–CH2Y and SiH2Y–CH2F (X = F, Cl, Br, I and Y = Cl, Br, I) in the Gas and Solution Phases

The gauche and trans rotamers of halogeno(halogenomethyl)silane (XSiH2CH2X; X = F, Cl, Br, I), fluoro(halogenomethyl)silane and halogeno(fluoromethyl)silane (SiH2F–CH2Y and SiH2Y–CH2F; Y = Cl, Br, I) have been studied in the gas phase using theoretical methods. The transition state arising from gauche-trans isomerization has also been modeled. The methods used are density functional theory (DFT) and second-order Moller–Plesset theory (MP2). B3LYP is the functional used for the DFT method. The basis set used is 6-311++G(d,p) for all atoms except that 6-311G(d,p) is used for the iodine atom only. The results indicate that the trans conformers are preferred in the gas phase and both energy difference and rotational barrier height increase as the size of the halogen increases. This study has been extended to include the solvent effect with the dielectric constant of the solvents varying from 2 to 80. The solvent effect was explored using Self-Consistent Reaction Field and the conformers have been fully optimized at the DFT/B3LYP level of theory. The net effect of a solvent is that energy difference decreases but the rotational barrier is not much affected. The findings from this work are explained in terms of different interactions and these are supported by a Natural Bond Orbital analysis.

Fine grained sampling of residue characteristics using molecular dynamics simulation

In a fine-grained computational analysis of protein structure, we investigated the relationships between a residue's backbone conformations and its side-chain packing as well as conformations. To produce continuous distributions in high resolution, we ran molecular dynamics simulations over a set of protein folds (dynameome). In effect, the dynameome dataset samples not only the states well represented in the PDB but also the known states that are not well represented in the structural database. In our analysis, we characterized the mutual influence among the backbone ϕ, ψ angles with the first side-chain torsion angles ( χ 1) and the volumes occupied by the side-chains. The dependencies of these relationships on side-chain environment and amino acids are further explored. We found that residue volumes exhibit dependency on backbone 2° structure conformation: side-chains pack more densely in extended β-sheet than in α-helical structures. As expected, residue volumes on the protein surface were larger than those in the interior. The first side-chain torsion angles are found to be dependent on the backbone conformations in agreement with previous studies, but the dynameome dataset provides higher resolution of rotamer preferences based on the backbone conformation. All three gauche −, gauche +, and trans rotamers show different patterns of ϕ, ψ dependency, and variations in χ 1 value are skewed from their canonical values to relieve the steric strains. By demonstrating the utility of dynameomic modeling on the native state ensemble, this study reveals details of the interplay among backbone conformations, residue volumes and side-chain conformations.

First principle study of the trans and gauche rotamers of 1,2dihalogenodisilanes (XSiH2SiH2X; X=F, Cl, Br and I) in vacuum

Abstract The trans and gauche rotamers of 1,2-dihalogenodisilanes (XSiH2SiH2X; X=F, Cl, Br and I) have been studied in the gas phase using theoretical methods. The transition state arising from the trans-gauche isomerisation has also been modelled. The methods used are second order Moller-Plesset theory (MP2) and density functional theory (DFT). The basis set used is 6-311 ++G(d,p) for all atoms except that 6-311G(d,p) has been used for iodine atom only. B3LYP is the functional used for the DFT method and G2/MP2 and CCSD(T) computations have also carried out using the MP2 optimised structures. All the computations have been done using Gaussian 03W. All the structures have been fully optimised and the optimised geometries, dipole moments, moment of inertia and energies are reported. Energies of the optimised structures have been used to obtain the energy difference between the trans and gauche rotamers and the barrier of rotation. The optimised structures have been used for computations of vibrational frequencies and these frequencies are reported with appropriate assignments. It is found that the trans conformers are preferred and both the energy difference and rotational barrier increase as the size of the halogen increases. These observations have been interpreted in terms of steric or electrostatic repulsion and antiperiplanar hyperconjugation supported with NBO analysis. The findings from this work have also been compared with the analogous 1,2-dihalogenoethanes. Some of the predicted parameters compare satisfactorily with those reported in literature. The theoretical rate constant for the trans rotamer-transition state isomerisation is reported for the first time for this type of interconversion. The literature for these compounds is limited in terms of conformational investigations and therefore the data from this work should serve as a useful set for reference.

Influence of glucose-templated proline mimetics on the β-turn conformation of the peptide fragment Ac-Leu- d-Phe-Pro-Val-NMe 2 found in Gramicidin S

The synthesis of tetrapeptide-based β-turn mimetics containing spirocyclic glucose-templated 3-hydroxyproline hybrids Glc3′( S)-5′( R)(CH 2OH)HypH and Glc3′( S)-5′( S)(CH 2OH)HypH as proline mimetics is presented. NMR-based conformational analysis of Ac-Leu- d-Phe-[Glc3′( S)-5′( R)(CH 2OH)HypH]-Val-NMe 2 and Ac-Leu- d-Phe-[Glc3′( S)-5′( S)(CH 2OH)HypH]-Val-NMe 2 demonstrates the presence of β-turn conformations. Different turn structures were observed by changing the stereochemistry at 5′-position of Glc3′( S)-5′( R)(CH 2OH)HypH. The major prolyl amide cis isomer of glucose-protected tetrapeptide Ac-Leu- d-Phe-[Glc(MOM) 43′( S)-5′( R)(CH 2OMOM)HypH]-Val-NMe 2 11 and glucose unprotected Ac-Leu- d-Phe-[Glc3′( S)-5′( R)(CH 2OH)HypH]-Val-NMe 2 13 forms a type VI β-turn conformation. In contrast, the major prolyl amide trans rotamer of tetrapeptide Ac-Leu- d-Phe-[Glc(MOM) 43′( S)-5′( S)(CH 2OMOM)HypH]-Val-NMe 2 12 conserves a similar β-turn conformation as the Gramicidin S-based peptide fragment Ac-Leu- d-Phe-Pro-Val-NMe 2 16.

Mass-analyzed Threshold Ionization Spectroscopy of Rotamers ofp-ethoxyphenol Cations and Configuration Effect

Two-color resonant two-photon mass-analyzed threshold ionization (MATI) spectroscopy was used to record the vibrationally resolved cation spectra of the selected rotamers of p-ethoxyphenol. The adiabatic ionization energies of the trans and cis rotamers are determined to be 61565 5 and 61670 5 cm1, which are less than that of p-methoxyphenol by 645 and 643 cm1, respectively. Analysis on the MATI spectra of the selected rotamers of p-ethoxyphenol cation shows that the relative orientation of the ethoxy group has little effect on the in-plane ring vibrations. The low-frequency OC2H5 bending vibrations appear to be active for both forms of the cation.

High Level ab Initio Energies and Structures for the Rotamers of 1,3-Butadiene

High level ab initio calculations, utilizing coupled cluster theory with quasi-perturbative triple excitations and augmented quadruple zeta level basis sets, have been used to determine the structures and relative energies of the four stationary points on the 1,3-butadiene torsional potential curve. Corrections were applied in order to minimize the residual basis set error, as well as account for core/valence correlation and scalar relativistic effects. Higher order correlation recovery was also included to improve our estimate of the relative energies. The transition state separating the trans and gauche rotamers lies 26.8 kJ/mol above the trans global minimum. The gauche rotamer lies 12.6 kJ/mol above the trans rotamer and the s-cis form is a transition state 2.0 kJ/mol higher than the gauche rotamer (excluding zero point energies).

Experimental and theoretical Raman and surface‐enhanced Raman scattering study of cysteine

AbstractRaman spectra in solid and 1 M solution of L‐cysteine and surface‐enhanced Raman scattering (SERS) spectra of this molecule in the zwitterionic form, by using colloidal silver nanoparticles, have been recorded. Density functional theory with the B3LYP functional was used for the optimizations of the ground state geometries and simulation of the vibrational spectrum of this amino acid. The SERS spectrum with a large silver cluster as a model metallic surface was simulated for the first time. Taking into account the experimental and calculated Raman and SERS vibrations and the corresponding assignments, as well as a comparison of force constants and geometrical parameters between the free zwitterion cysteine and the one in the presence of the colloidal silver nanoparticles, we can confirm the presence of gauche (PH) and trans (PN) rotamers in the solid state, the formation of a SS bond in the solution state, the dissociation of the peptide bond and mixing of rotamers because of the SERS effect, and the relative importance of the interaction of sulphyldryl, NH3+, and carboxylate groups with the metallic surface. Copyright © 2009 John Wiley & Sons, Ltd.

UV Resonant Two-Photon Ionization Spectrum of 1-Naphthol

The resonant two-photon ionization(R2PI) spectrum of 1-naphthol(1NP) was studied from 305 to 322 nm using supersonic molecular beam technique.1NP has two rotamers:cis and trans.The R2PI spectrum was used to characterize the S1←S0 transition of the trans species and its original band appeared at 317.8 nm(31456 cm-1).The vibrational bands of the trans species from the R2PI spectrum can be assigned to in-plane vibrational modes with a′ symmetry.Ab initio and density functional theory(DFT) calculations indicate that the cis rotamer has higher energy than the trans rotamer by 439 cm-1 in the ground state but it has a lower exciting energy than the trans rotamer by 1216 cm-1 for the S1 ←S0 transition.These calculated results are in good agreement with the experimental trend where the difference between the cis and trans energies in the S0 state is 220 cm-1 and the difference between the cis and trans exciting energies is 274 cm-1.There are no spectral features from the cis rotamer in the R2PI spectrum and we attribute this to the efficient cooling conditions in the molecular beam,which leads to a very small cis rotamer population with the higher energy(220 cm-1).

An Investigation of the Rotamers of Butadiene by High-Resolution Infrared Spectroscopy

A wide-ranging investigation of high-resolution infrared spectra of 1,3-butadiene was undertaken with the prime objective of finding subbands in the rotational structure attributable to the gauche rotamer, from which information about the molecular structure could be derived. A weak band near 750 cm(-1), which had previously been assigned to the gauche rotamer, has been shown to be a difference band for the trans rotamer. In support of the analysis of this band, the rotational structure, including two hot bands, was analyzed in the C-type band for the nu(12)(a(u)) mode near 525 cm(-1) and in the C-type band near 162 cm(-1) for the nu(13)(a(u)) mode. An unsuccessful attempt was made to extend the analysis of the B-type component of the A/B-type band for nu(17)(b(u)) near 3000 cm(-1). With the exception of the two weak Q branches at 463.82 and 462.16 cm(-1), no new evidence for the gauche rotamer in the gas phase was found.

The role of nanoclay in the generation of poly(ethylene terephthalate) fibers with improved modulus and tenacity

The effect of nanoclay concentration on the molecular orientation and drawability of poly(ethylene terephthalate) PET was examined using thermal and vibrational spectroscopic analysis. Although drawability at 83°C in hot air increased by the addition of nanoclay, the maximum draw ratio was independent of nanoclay concentration. The average molecular orientation of the PET chain was found to mimic the trend in mechanical property improvements. Both Young's modulus and tenacity (i.e. strength) showed the maximum improvement at a 1wt% loading of clay, which was shown to coincide with the maximum amount of molecular orientation. Nanoclay was shown to intercalate with PET and enhanced amorphous orientation that led to modulus and strength improvements. However, at higher concentrations of nanoclay the presence of large agglomerates prevented efficient orientation to the fiber axis and acted as stress concentrators to aid in cavitation and failure during testing. Raman spectroscopy showed that the as-spun unfilled PET fibers possessed significantly more trans rotamer content of the ethylene glycol moiety than the nanocomposite fibers.

Submillimeter Spectrum of Formic Acid

We have measured new submillimeter-wave data around 600 GHz and around 1.1 THz for the 13C isotopologue of formic acid and for the two deuterium isotopomers; in each case for both the trans and cis rotamer. For cis-DCOOH and cis-HCOOD in particular only data up to 50 GHz was previously available. For all species the quality and quantity of molecular parameters has been increased, providing new measured frequencies and more precise and reliable frequencies in the range of existing and near-future submillimeter and far-infrared astronomical spectroscopy instruments such as Herschel, SOFIA, and ALMA.

Conformational Domino Effect in Saccharides: A Prediction from Alkyl β-(1→6)-Diglucopyranosides

A series of alkyl beta-D-glucopyranosyl-(1-->6)-beta-D-glucopyranosides, containing nonchiral and chiral aglycons, were synthesized and analyzed by NMR and CD. The results, collected from four sets of disaccharides, demonstrated that the rotational properties of the interglycosidic linkage depend on the structural natures of both the aglycon and the solvent. Stereoelectronic and steric factors explain this rotational dependence, the gauche- trans (gt) rotamer being the most stable. Furthermore, correlations between Taft's steric parameters or between the pKa values of the alkyl substituent (aglycon) versus corresponding rotamer populations were observed. These results point to a natural conformational domino effect in oligosaccharides, where the conformational properties of each (1-->6) interglycosidic linkage will depend on the structure of the previous residue or its aglycon. In addition, a very weak rotational population dependence of the hydroxymethyl group at residue II on the aglycon at residue I was observed. The population of the gauche- gauche (gg) rotamer decreased, and that of gt increased as the Taft's steric parameters of the remote aglycon increased, independently of the disaccharide series and of the solvent.